The field of human genetics has been revolutionized by the development of a large collection of restriction fragment length polymorphisms (RFLPs). Even though there are now 2300 RFLPs characterized, there are only 500 polymorphisms in coding genes. Thus, there is a need to develop new methods to allow polymorphisms to be characterized in specific genes. We have characterized a number of polymorphisms in biologically important human genes using both standard approaches, as well as new methods that employ the polymerase chain reaction (PCR). Polymorphisms have been described in a gene that alters the morphology of papillomavirus transformed cells (pl596); and the immunoglobulin Fc receptor, which can also serve as a receptor for HIV. The PCR has been employed to amplify specific regions of genes, such as the introns or the 3' untranslated region. The resulting DNA products are then assayed for variation by one of four approaches: (1) digestion with frequently cutting (4 base pair [bp] recognition site) enzymes; (2) analysis of simple sequence (microsatellite) loci on high resolution gels; (3) single-stranded conformation polymorphism (SSCP) analysis, a method for detecting single bp changes in DNA; or (4) heteroduplex analysis, a method developed by this project for detecting sequence variation. Using these approaches we have been able to identify and characterize polymorphisms in several different genes including the KIT oncogene, the insulin-like growth factor receptor 1, the dopamine D2 receptor, and the gamma aminobutyric acid receptor. All of these polymorphisms have been typed in the 40 large human pedigrees provided by the Centre D'Etude du Polymorphisme Humain for the construction of human genetic linkage maps. These methods should allow virtually any human gene to be developed as a genetic marker, and should greatly increase the possibility for understanding complex human disorders with at least a partial genetic basis.